PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing

Xiangbin Ruan, Kaining Hu and Xiaochang Zhang ()
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Xiangbin Ruan: University of Chicago
Kaining Hu: University of Chicago
Xiaochang Zhang: University of Chicago

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract RNA-binding proteins (RBPs) are essential for gene regulation, but it remains a challenge to identify their RNA targets across cell types. Here we present PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing by conjugating C-to-U and A-to-I base editors to RBPs. We benchmark PIE-Seq and demonstrate its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs. Bulk PIE-Seq identifies canonical binding features for RBPs such as PUM2 and NOVA1, and nominates additional target genes for most tested RBPs such as SRSF1 and TDP-43/TARDBP. Homologous RBPs frequently edit similar sequences and gene sets in PIE-Seq while different RBP families show distinct targets. Single-cell PIE-PUM2 uncovers comparable targets to bulk samples and applying PIE-PUM2 to the developing mouse neocortex identifies neural-progenitor- and neuron-specific target genes such as App. In summary, PIE-Seq provides an orthogonal approach and resource to uncover RBP targets in mice and human cells.

Date: 2023
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DOI: 10.1038/s41467-023-39054-8

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